I am planning to do a CNV calling for the first time and I've got Illumina single-read data (50bp). Libraries were not sequenced in paired-end because it is a bacterial genome so the coverage is very high even with single-read data (~400X).
I've read a lot of things about CNV calling and discovered that most of tools are designed for paired-end data.
I've read that there are different kind of methods depending on what the tool focus on : SR (Split Read : split misaligned paired reads), RP (Read Paired : uses insert sizes distribution), RD (Read Depth) and CA (Combinatory approach : takes advantages of all methods). The latest is the more confident and complete method, so that I would like to use a tool which use the CA method. But it seems that paired-end reads are always required and maybe I have no other choice than using a RD tool.
My question is: did someone already call CNV with single-read data, or does someone know which tool might be the best suited for?
I've read a lot of things about CNV calling and discovered that most of tools are designed for paired-end data.
I've read that there are different kind of methods depending on what the tool focus on : SR (Split Read : split misaligned paired reads), RP (Read Paired : uses insert sizes distribution), RD (Read Depth) and CA (Combinatory approach : takes advantages of all methods). The latest is the more confident and complete method, so that I would like to use a tool which use the CA method. But it seems that paired-end reads are always required and maybe I have no other choice than using a RD tool.
My question is: did someone already call CNV with single-read data, or does someone know which tool might be the best suited for?
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